10.1371/journal.pbio.3000958

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome
Cited by: 14
Author(s): Kai Ehrenbolger, Nathan Jespersen, Himanshu Sharma, Yuliya Y. Sokolova, Yuri S. Tokarev, Charles R. Vossbrinck, Jonas Barandun
Software Mentions: 3
Published: almost 6 years ago

10.3390/cancers13071618

Covalent Cysteine Targeting of Bruton’s Tyrosine Kinase (BTK) Family by Withaferin-A Reduces Survival of Glucocorticoid-Resistant Multiple Myeloma MM1 Cells
Cited by: 10
Author(s): Emilie Logie, Chandra Sekhar Chirumamilla, Claudina Pérez-Novo, Priyanka Shaw, Ken Declerck, Ajay Palagani, Savithri Rangarajan, Bart Cuypers, Nicolas De Neuter, Mobashar Hussain Urf Turabe Fazil, Navin Kumar Verma, Annemie Bogaerts, Kris Laukens, Fritz Offner, Pieter Van Vlierberghe, Xaveer Van Ostade, Wim Vanden Berghe
Software Mentions: 3
Published: over 5 years ago

10.3390/md16100386

Kororamides, Convolutamines, and Indole Derivatives as Possible Tau and Dual-Specificity Kinase Inhibitors for Alzheimer’s Disease: A Computational Study
Cited by: 25
Author(s): Laura Llorach-Parés, Alfons Nonell-Canals, Conxita Àvila, Melchor Sánchez-Martínez
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12859-017-1541-z

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP
Cited by: 24
Author(s): Julia Koehler Leman, Sergey Lyskov, Richard Bonneau
Software Mentions: 3
Published: over 9 years ago

10.1016/j.cell.2018.11.025

The Molecular Mechanism of Transport by the Mitochondrial ADP/ATP Carrier
Cited by: 206
Author(s): Jonathan J. Ruprecht, Martin King, Thomas Zögg, Antoniya A. Aleksandrova, Els Pardon, Paul G. Crichton, Jan Steyaert, Edmund R. S. Kunji
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41421-020-00215-4

A novel multistage antiplasmodial inhibitor targeting Plasmodium falciparum histone deacetylase 1
Cited by: 20
Author(s): Zhenghui Huang, Ruoxi Li, Tongke Tang, Dazheng Ling, Manjiong Wang, Dandan Xu, Maoxin Sun, Lulu Zheng, Feng Zhu, Hui Min, Rachasak Boonhok, Yan Ding, Yang Wen, Zhong Chen, Xiaokang Li, Yuxi Chen, Taiping Liu, Jiping Han, Jun Miao, Qiang Fang, Yaming Cao, Yun Tang, Jie Cui, Wei Xu, Liwang Cui, Jin Zhu, Gary Wong, Jian Li, Lubin Jiang
Software Mentions: 3
Published: almost 6 years ago

10.1155/2020/2758640

A Bioinformatics Research on Novel Mechanism of Compound Kushen Injection for Treating Breast Cancer by Network Pharmacology and Molecular Docking Verification
Cited by: 6
Author(s): Shuyu Liu, Xiaohong Hu, Xiaotian Fan, Ruiqi Jin, Wenqian Yang, Yifei Geng, Jiarui Wu
Software Mentions: 3
Published: about 6 years ago

10.1093/gbe/evv046

OASes and STING: Adaptive Evolution in Concert
Cited by: 38
Author(s): Alessandra Mozzi, Chiara Pontremoli, Diego Forni, Mario Clerici, Nereo Bresolin, Rachele Cagliani, Manuela Sironi
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-019-39641-0

Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H
Cited by: 13
Author(s): Chang Woo Lee, Sun Ha Park, Chang-Sung Jeong, Sun Mi Shin, Hyun Park, Jun Hyuck Lee
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-15-319

Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes
Cited by: 6
Author(s): Brian G. Pierce, Thom Vreven, Zhiping Weng
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0248394

Anti-asthmatic effect of nitric oxide metallo-donor FOR811A [cis-[Ru(bpy)2(2-MIM)(NO)](PF6)3] in the respiratory mechanics of Swiss mice
Cited by: 6
Author(s): Paula Priscila Correia Costa, Stefanie Bressan Waller, Gilvan Ribeiro dos Santos, Fladimir de Lima Gondim, Daniel Silveira Serra, Francisco Sales Ávila Cavalcante, Florêncio Sousa Gouveia Júnior, Valdir Ferreira de Paula Júnior, Eduardo Henrique Silva Sousa, Luiz Gonzaga de França Lopes, Wesley Lyeverton Correia Ribeiro, Helena Serra Azul Monteiro
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0191610

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii
Cited by: 1
Author(s): Bhumika S. Shah, Heather E. Ashwood, S.J. Harrop, Daniel N. Farrugia, Ian T. Paulsen, Bridget C. Mabbutt
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0105984

Cleavage Specificity Analysis of Six Type II Transmembrane Serine Proteases (TTSPs) Using PICS with Proteome-Derived Peptide Libraries
Cited by: 46
Author(s): Olivier Barré, Antoine Dufour, Ulrich Eckhard, Reinhild Kappelhoff, François Béliveau, Richard Leduc, Christopher M. Overall
Software Mentions: 2
Published: about 12 years ago

10.1107/S2053230X14003355

A range of C∊3–C∊4 interdomain angles in IgE Fc accommodate binding to its receptor CD23
Cited by: 13
Author(s): B. Dhaliwal, M.O.Y. Pang, Daopeng Yuan, Andrew J. Beavil, Brian J. Sutton
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0226657

Biophysical analysis of Plasmodium falciparum Hsp70-Hsp90 organising protein (PfHop) reveals a monomer that is characterised by folded segments connected by flexible linkers
Cited by: 11
Author(s): Stanley Makumire, Tawanda Zininga, Juha Vahokoski, Inari Kursula, Addmore Shonhai
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0232757

Characterization of a human monoclonal antibody generated from a B-cell specific for a prefusion-stabilized spike protein of Middle East respiratory syndrome coronavirus
Cited by: 10
Author(s): Jang Hoon Choi, Hye Min Woo, Tae Young Lee, So Young Lee, Sang Mu Shim, Woo Jung Park, Jeong Sun Yang, Joo Ae Kim, Mi Ran Yun, Dae Won Kim, Sung Soon Kim, Yi Zhang, Wei Shi, Lingshu Wang, Barney S. Graham, John R. Mascola, Nanshuang Wang, Jason S. McLellan, Joo Yeon Lee, Hansaem Lee
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0122512

Crystal Structure of a Two-Subunit TrkA Octameric Gating Ring Assembly
Cited by: 2
Author(s): Marc C. Deller, Hope A. Johnson, Mitchell D. Miller, Glen Spraggon, Marc‐André Elsliger, Ian A. Wilson, Scott A. Lesley
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0103099

In Silico Modeling of Human α2C-Adrenoreceptor Interaction with Filamin-2
Cited by: 11
Author(s): Marcin Pawłowski, Saras Saraswathi, Hanaa K. B. Motawea, Maqsood A. Chotani, Andrzej Kloczkowski
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0041710

Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions
Cited by: 21
Author(s): T.A. Binkowski, Susana R. Marino, A. Joachimiak
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0140984

Improving the pH-stability of Versatile Peroxidase by Comparative Structural Analysis with a Naturally-Stable Manganese Peroxidase
Cited by: 40
Author(s): Verónica Sáez-Jiménez, Elena Fernández‐Fueyo, F.J. Medrano, Antonio Romero, Ángel T. Martínez, Francisco J. Ruíz-Dueñas
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0052066

Structural and Functional Insights into (S)-Ureidoglycolate Dehydrogenase, a Metabolic Branch Point Enzyme in Nitrogen Utilization
Cited by: 4
Author(s): Myungil Kim, Inchul Shin, Suhee Cho, Jee Hyun Lee, Sangkee Rhee
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0245358

Insights into structure and dynamics of extracellular domain of Toll-like receptor 5 in Cirrhinus mrigala (mrigala): A molecular dynamics simulation approach
Cited by: 8
Author(s): Ajaya Kumar Rout, Varsha Acharya, Diptimayee Maharana, Budheswar Dehury, Sheela Rani Udgata, Rajkumar Jena, Bhaskar Behera, Pranaya Kumar Parida, Bijay Kumar Behera
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0026278

A Novel Metagenomic Short-Chain Dehydrogenase/Reductase Attenuates Pseudomonas aeruginosa Biofilm Formation and Virulence on Caenorhabditis elegans
Cited by: 108
Author(s): P. Bijtenhoorn, Hubert Mayerhofer, Jochen Müller-Dieckmann, Christian Utpatel, Christina Schipper, C. Hornung, Matthias Szesny, Stephanie Grond, Andrea Thürmer, Elżbieta Brzuszkiewicz, Rolf Daniel, Katja Dierking, Hinrich Schulenburg, Wolfgang R. Streit
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0123996

Novel Non-Peptide Inhibitors against SmCL1 of Schistosoma mansoni: In Silico Elucidation, Implications and Evaluation via Knowledge Based Drug Discovery
Cited by: 5
Author(s): Atif Zafar, Sameena Ahmad, Asim Rizvi, Masood Ahmad
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0195355

Solution scattering study of the Bacillus subtilis PgdS enzyme involved in poly-γ-glutamic acids degradation
Cited by: 1
Author(s): Jumei Zeng, Yipeng Jin, Zhongchuan Liu
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0196642

Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance
Cited by: 9
Author(s): Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean Johnson
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0042473

Crystal Structures of the Network-Forming Short-Arm Tips of the Laminin β1 and γ1 Chains
Cited by: 51
Author(s): Federico Carafoli, Sadaf-Ahmahni Hussain, Erhard Hohenester
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0201556

Deciphering the targets of retroviral protease inhibitors in Plasmodium berghei
Cited by: 16
Author(s): Noah Machuki Onchieku, Reagan M. Mogire, Loise Ndung’u, Peter Mwitari, Francis Kimani, Damaris Matoke-Muhia, Daniel Kiboi, Gabriel Magoma
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0235990

Drug targeting CYP2E1 for the treatment of early-stage alcoholic steatohepatitis
Cited by: 18
Author(s): Torsten Diesinger, Vyacheslav Buko, Alfred Lautwein, Radovan Dvorský, Elena Belonovskaya, Oksana Lukivskaya, Elena Naruta, Siarhei Kirko, В. П. Андреев, Dominik Buckert, Sebastian Bergler, Christian Renz, Edith Schneider, Florian Kuchenbauer, Mukesh Kumar, Çagatay Güneş, Berthold Büchele, Thomas Simmet, Dieter Müller‐Enoch, Thomas Wirth, Thomas Haehner
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0069833

An Activating Mutation Reveals a Second Binding Mode of the Integrin α2 I Domain to the GFOGER Motif in Collagens
Cited by: 29
Author(s): Federico Carafoli, Samir Hamaia, Dominique Bihan, Erhard Hohenester, Richard W. Farndale
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0216979

Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis
Cited by: 2
Author(s): Ke Shi, Chong-Min Kyung, Kelly G. Aukema, Thomas Lee, Asim K. Bera, Jennifer L. Seffernick, Lawrence P. Wackett, Hideki Aihara
Software Mentions: 2
Published: over 7 years ago

10.1107/S1399004715002485

Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6β4
Cited by: 38
Author(s): Noelia Alonso-García, Inés García-Rubio, José A. Manso, Rubén M. Buey, Hector Urien, Arnoud Sonnenberg, Gunnar Jeschke, José M. de Pereda
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0215555

Heavy-atom labeling of RNA by PLOR for de novo crystallographic phasing
Cited by: 6
Author(s): Jason R. Stagno, Ping Yü, Marcin Dyba, Yun‐Xing Wang, Yu Liu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0121494

Crystal Structures of the Kinase Domain of the Sulfate-Activating Complex in Mycobacterium tuberculosis
Cited by: 9
Author(s): Ömer Poyraz, Katharina Brunner, Bernhard Lohkamp, Hanna Axelsson, Lars G.J. Hammarström, R. Schnell, Günter Schneider
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0104878

Molecular Analysis of Aedes aegypti Classical Protein Tyrosine Phosphatases Uncovers an Ortholog of Mammalian PTP-1B Implicated in the Control of Egg Production in Mosquitoes
Cited by: 7
Author(s): Débora Monteiro Moretti, Lalima G. Ahuja, Rodrigo Dutra Nunes, Cecília Oliveira Cudischevitch, Carlos Renato de Oliveira Daumas-Filho, Priscilla Medeiros-Castro, Guilherme Ventura-Martins, Willy Jablonka, Felipe Gazos-Lopes, Raquel Senna, Marcos Henrique Ferreira Sorgine, Klaus Hartfelder, Margareth Lara Capurro, Geórgia C. Atella, Rafael D. Mesquita, Mário A.C. Silva-Neto
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0167755

Biophysical Studies of the Induced Dimerization of Human VEGF Receptor 1 Binding Domain by Divalent Metals Competing with VEGF-A
Cited by: 10
Author(s): Jonathan Gaucher, Marie Reille‐Seroussi, Nathalie Gagey‐Eilstein, Sylvain Broussy, Pascale Coric, Bili Seijo, Marie-Bernard Lascombe, Benoît Gautier, Wang-Quing Liu, Florent Huguenot, Nicolas Inguimbert, Serge Bouaziz, Michel Vidal, Isabelle Broutin
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0052642

Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases
Cited by: 6
Author(s): Cédric Grauffel, Angèle Abboud, Glen Liszczak, Ronen Marmorstein, Thomas Arnesen, Nathalie Reuter
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0017624

Structure and Function of the First Full-Length Murein Peptide Ligase (Mpl) Cell Wall Recycling Protein
Cited by: 24
Author(s): Debanu Das, Mireille Hervé, Julie Feuerhelm, Carol L. Farr, Hsiu‐Ju Chiu, Marc‐André Elsliger, Mark W. Knuth, Heath E. Klock, Mitchell D. Miller, Adam Godzik, Scott A. Lesley, Ashley M. Deacon, Dominique Mengin‐Lecreulx, Ian A. Wilson
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0074788

The Structural Basis of Erwinia rhapontici Isomaltulose Synthase
Cited by: 17
Author(s): Zheng Xu, Sha Li, Jie Li, Yan Li, Xiaohai Feng, Renxiao Wang, Hong Xu, Jiahai Zhou
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0223464

Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding
Cited by: 15
Author(s): Rumbidzai Chitongo, Adetayo Emmanuel Obasa, Sello Given Mikasi, Graeme Brendon Jacobs, Ruben Cloete
Software Mentions: 2
Published: over 6 years ago

10.1107/S2059798320008049

Fragment-based determination of a proteinase K structure from MicroED data using <i>ARCIMBOLDO_SHREDDER</i>
Cited by: 12
Author(s): Logan S. Richards, Claudia Millán, Jennifer Miao, Michael W. Martynowycz, M.R. Sawaya, Tamir Gonen, Rafael J. Borges, Isabel Usón, José A. Rodríguez
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0160694

Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA
Cited by: 15
Author(s): Yinglu Zhang, Katarzyna Rataj, Gordon G. Simpson, Liang Tong
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0072368

SCMCRYS: Predicting Protein Crystallization Using an Ensemble Scoring Card Method with Estimating Propensity Scores of P-Collocated Amino Acid Pairs
Cited by: 73
Author(s): Phasit Charoenkwan, Watshara Shoombuatong, Hua Chin Lee, Jeerayut Chaijaruwanich, Hui Ling Huang, Shinn‐Ying Ho
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0186840

Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins
Cited by: 11
Author(s): Mykhaylo O. Debelyy, Patrice Waridel, Manfredo Quadroni, Roger Schneiter, Andreas Conzelmann
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0175723

Soaking suggests “alternative facts”: Only co-crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating a novel mode-of-inhibition
Cited by: 31
Author(s): F.R. Ehrmann, Johann Stojko, A. Metz, François Debaene, Luzi Jakob Barandun, A. Heine, François Diederich, Sarah Cianférani, Klaus Reuter, G. Klebe
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0023582

Flanking Bases Influence the Nature of DNA Distortion by Platinum 1,2-Intrastrand (GG) Cross-Links
Cited by: 18
Author(s): Debadeep Bhattacharyya, Srinivas Ramachandran, Sanjai Sharma, Wimal Pathmasiri, Candice L. King, Irene Abraham, Gunnar Boysen, James A. Swenberg, Sharon L. Campbell, Nikolay V. Dokholyan, Stephen G. Chaney
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0043019

Structures of Human DPP7 Reveal the Molecular Basis of Specific Inhibition and the Architectural Diversity of Proline-Specific Peptidases
Cited by: 23
Author(s): G.A. Bezerra, E. Dobrovetsky, Aiping Dong, Almagul Seitova, Lissete Crombett, Lisa M. Shewchuk, Annie M. Hassell, Sharon Sweitzer, Thomas D. Sweitzer, Patrick McDevitt, Kyung Johanson, Karen M. Kennedy-Wilson, D. Cossar, A. Bochkarev, Karl Gruber, Sirano Dhe‐Paganon
Software Mentions: 2
Published: about 14 years ago

10.1007/s00253-021-11129-w

Assembly of a Rieske non-heme iron oxygenase multicomponent system from Phenylobacterium immobile E DSM 1986 enables pyrazon cis-dihydroxylation in E. coli
Cited by: 4
Author(s): Andreas Hunold, Wendy Escobedo‐Hinojosa, Elsa Potoudis, Daniela Resende, Theresa Farr, Per‐Olof Syrén, Bernhard Hauer
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0201234

How does binding of agonist ligands control intrinsic molecular dynamics in human NMDA receptors?
Cited by: 5
Author(s): Zoltan Palmai, Kimberley Houenoussi, Sylvia Cohen‐Kaminsky, Luba Tchertanov
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0036526

Structural Analyses of the Slm1-PH Domain Demonstrate Ligand Binding in the Non-Canonical Site
Cited by: 21
Author(s): K. Anand, Kenji Maeda, Anne‐Claude Gavin
Software Mentions: 2
Published: over 14 years ago

10.1107/S2059798318005764

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation
Cited by: 6
Author(s): Pavel V. Afonine, Paul D. Adams, Alexandre Urzhumtsev
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0255167

pyProGA—A PyMOL plugin for protein residue network analysis
Cited by: 8
Author(s): Vladimı́r Sládek, Yuta Yamamoto, Ryuhei Harada, Mitsuo Shoji, Yasuteru Shigeta
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0067158

Characterization of PUD-1 and PUD-2, two proteins up-regulated in a long-lived daf-2 mutant.
Cited by: 8
Author(s): Yue-He Ding, Yunguang Du, Shukun Luo, Yuxin Li, Tie-Mei Li, Sawako Yoshina, Xing Wang, Karsten Klage, Shohei Mitani, Keqiong Ye, Meng‐Qiu Dong
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0106936

Atomic Resolution Structure of a Protein Prepared by Non-Enzymatic His-Tag Removal. Crystallographic and NMR Study of GmSPI-2 Inhibitor
Cited by: 8
Author(s): Edyta Kopera, Wojciech Bal, Martina Lenarčič Živković, A. S. Dvornyk, Barbara Kłudkiewicz, Krystyna Grzelak, Igor Zhukov, Włodzimierz Zagórski-Ostoja, Mariusz Jaskólski, Szymon Krzywda
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0006820

The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF
Cited by: 17
Author(s): Zamia Diaz, Karina B. Xavier, Stephen T. Miller
Software Mentions: 2
Published: about 17 years ago

10.1007/s00253-017-8161-4

Trichoderma reesei xylanase 5 is defective in the reference strain QM6a but functional alleles are present in other wild-type strains
Cited by: 8
Author(s): Jonas Ramoni, Martina Marchetti‐Deschmann, Verena Seidl‐Seiboth, Bernhard Schink
Software Mentions: 2
Published: over 9 years ago

10.1007/s13205-014-0216-y

Computational pipeline to identify and characterize functional mutations in ornithine transcarbamylase deficiency
Cited by: 6
Author(s): R. Magesh, C. George Priya Doss
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0040066

The Crystal Structures of Dystrophin and Utrophin Spectrin Repeats: Implications for Domain Boundaries
Cited by: 27
Author(s): M. Muthu, Kylie A. Richardson, Andrew J. Sutherland-Smith
Software Mentions: 2
Published: about 14 years ago

10.1107/S2059798319006831

Structural and functional characterization of CMP-<i>N</i>-acetylneuraminate synthetase from<i>Vibrio cholerae</i>
Cited by: 1
Author(s): Sucharita Bose, Debayan Purkait, Deepthi Joseph, Vinod Nayak, Ramaswamy Subramanian
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0015199

Tracing the Origin of the Fungal α1 Domain Places Its Ancestor in the HMG-Box Superfamily: Implication for Fungal Mating-Type Evolution
Cited by: 92
Author(s): Tom Martin, Shunwen Lu, Herman van Tilbeurgh, Daniel R. Ripoll, Christina Dixelius, B. Gillian Turgeon, Robert Debuchy
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0118684

How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Cited by: 42
Author(s): Luciano A. Abriata, Timothy Palzkill, Matteo Dal Peraro
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0063370

Structural Basis for the Oligomerization-State Switch from a Dimer to a Trimer of an Engineered Cortexillin-1 Coiled-Coil Variant
Cited by: 2
Author(s): Saša Bjelić, Mara M. Wieser, Daniel Frey, Christian U. Stirnimann, Mark R. Chance, Rolf Jaussi, Michel O. Steinmetz, Richard A. Kammerer
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0124272

LucY: A Versatile New Fluorescent Reporter Protein
Cited by: 4
Author(s): M.E. Auldridge, Heidi B. Cao, Satyabrata Sen, Laura Franz, C.A. Bingman, Ragothaman M. Yennamalli, George N. Phillips, David A. Mead, Eric J. Steinmetz
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0193028

Folic acid derived-P5779 mimetics regulate DAMP-mediated inflammation through disruption of HMGB1:TLR4:MD-2 axes
Cited by: 13
Author(s): Shan Sun, Mingzhu He, Yongjun Wang, Huan Yang, Yousef Al‐Abed
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0025376

Putting into Practice Domain-Linear Motif Interaction Predictions for Exploration of Protein Networks
Cited by: 37
Author(s): Katja Luck, Sadek Fournane, Bruno Kieffer, Murielle Masson, Yves Nominé, Gilles Travé
Software Mentions: 2
Published: almost 15 years ago

10.1128/AEM.00390-19

Versatile Oxidase and Dehydrogenase Activities of Bacterial Pyranose 2-Oxidase Facilitate Redox Cycling with Manganese Peroxidase <i>In Vitro</i>
Cited by: 18
Author(s): Peter L. Herzog, Leander Sützl, Beate Eisenhut, Daniel Maresch, Dietmar Haltrich, Christian Obinger, Clemens K. Peterbauer
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0143876

The First Extracellular Domain Plays an Important Role in Unitary Channel Conductance of Cx50 Gap Junction Channels
Cited by: 12
Author(s): Xiaoling Tong, Hiroshi Aoyama, Swathy Sudhakar, Honghong Chen, Brian H. Shilton, Donglin Bai
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0248634

Prediction of LncRNA-encoded small peptides in glioma and oligomer channel functional analysis using in silico approaches
Cited by: 6
Author(s): Yipeng Cao, Rui Yang, Imshik Lee, Wenwen Zhang, Jiana Sun, Xiangfei Meng, Wei Wang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0091232

Molecular Recognition of the Neurotransmitter Acetylcholine by an Acetylcholine Binding Protein Reveals Determinants of Binding to Nicotinic Acetylcholine Receptors
Cited by: 34
Author(s): Jeppe Olsen, Thomas Balle, Michael Gajhede, Philip K. Ahring, J.S. Kastrup
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0064363

Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability
Cited by: 65
Author(s): Bryan S. Der, Christien Kluwe, Aleksandr E. Miklos, Ron Jacak, Sergey Lyskov, Jeffrey J. Gray, George Georgiou, Andrew D. Ellington, Brian Kuhlman
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0195442

An antibody with Fab-constant domains exchanged for a pair of CH3 domains
Cited by: 9
Author(s): Gordana Wozniak‐Knopp, Gerhard Stadlmayr, Jan Walther Perthold, Katharina Stadlbauer, Mathias Gotsmy, Stefan Becker, Florian Rüker
Software Mentions: 2
Published: over 8 years ago

10.1128/AEM.01692-19

Crystal Structure of the Catalytic and Cytochrome <i>b</i> Domains in a Eukaryotic Pyrroloquinoline Quinone-Dependent Dehydrogenase
Cited by: 15
Author(s): Kouta Takeda, Takuya Ishida, Makoto Yoshida, Masahiro Samejima, Hiroyuki Ohno, Kiyohiko Igarashi, Nobuhumi Nakamura
Software Mentions: 2
Published: almost 7 years ago

10.1107/S2059798319010027

Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX
Cited by: 11
Author(s): Katarina Koruza, Bénédicte Lafumat, Maria Nyblom, Brian P. Mahon, Wolfgang Knecht, Robert McKenna, S.Z. Fisher
Software Mentions: 2
Published: about 7 years ago

10.1107/S2059798315023116

Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects
Cited by: 11
Author(s): Christian Reichen, Chaithanya Madhurantakam, Simon Hansen, Markus G. Grütter, Andreas Plückthun, Peer R. E. Mittl
Software Mentions: 2
Published: almost 11 years ago

10.1107/S0907444910007493

Features and development of <i>Coot</i>
Cited by: 21,554
Author(s): Paul Emsley, Bernhard Lohkamp, William G. Scott, Kevin Cowtan
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0184627

Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38α MAPK
Cited by: 10
Author(s): Mike Bührmann, Bianca Wiedemann, Matthias Müller, Julia Hardick, Mary Ecke, Daniel Rauh
Software Mentions: 2
Published: about 9 years ago

10.1107/S2059798317018289

The deduced role of a chitinase containing two nonsynergistic catalytic domains
Cited by: 16
Author(s): Tian Liu, Weixing Zhu, Jing Wang, Yong Zhou, Yanwei Duan, Mingli Qu, Qing Yang
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0085940

Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site
Cited by: 47
Author(s): Young Do Kwon, Judith M. LaLonde, Yongping Yang, Mark A. Elban, Akihiro Sugawara, Joel R. Courter, David M. Jones, Amos B. Smith, Asim K. Debnath, Peter D. Kwong
Software Mentions: 2
Published: over 12 years ago

10.1107/S0907444913011438

Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement
Cited by: 7
Author(s): Debora L. Makino, Elena Conti
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0075446

A Purine Analog Synergizes with Chloroquine (CQ) by Targeting Plasmodium falciparum Hsp90 (PfHsp90)
Cited by: 23
Author(s): Dea Shahinas, Asongna Folefoc, Tony Taldone, Gabriela Chiosis, Ian Crandall, Dylan R. Pillai
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0134084

Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes
Cited by: 12
Author(s): Radhika Ganu, Yasuko Ishida, Markos Koutmos, Sergios‐Orestis Kolokotronis, Alfred L. Roca, Timothy A. Garrow, Lawrence B. Schook
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0234869

Whole-genome sequencing reveals origin and evolution of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018
Cited by: 7
Author(s): Xiaonan Zhao, Han-Ju Zhang, Duo Li, Ji Zhou, Y. Chen, Yanhong Sun, Adeniyi C. Adeola, Xiaoqing Fu, Yong Shao, Meiling Zhang
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0128310

Structural Studies of the HIV-1 Integrase Protein: Compound Screening and Characterization of a DNA-Binding Inhibitor
Cited by: 15
Author(s): Peter K. Quashie, Ying-Shan Han, Said Hassounah, Thibault Mésplède, Mark A. Wainberg
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0174284

Structural insights into the regulation of Bacillus subtilis SigW activity by anti-sigma RsiW
Cited by: 19
Author(s): Shankar Raj Devkota, Eunju Kwon, Soonhoi Ha, Hyeun Wook Chang, Dong Young Kim
Software Mentions: 2
Published: over 9 years ago

10.1007/s13205-014-0274-1

Structure-based function analysis of putative conserved proteins with isomerase activity from Haemophilus influenzae
Cited by: 13
Author(s): Mohd Shahbaaz, Faizan Ahmad
Software Mentions: 2
Published: almost 12 years ago

10.1107/S2059798317015236

The crystal structure of the<i>Yersinia pestis</i>iron chaperone YiuA reveals a basic triad binding motif for the chelated metal
Cited by: 5
Author(s): C.D. Radka, Dongquan Chen, Lawrence J. DeLucas, Stephen G. Aller
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0026021

Structural and Biochemical Studies of Human 4-hydroxy-2-oxoglutarate Aldolase: Implications for Hydroxyproline Metabolism in Primary Hyperoxaluria
Cited by: 49
Author(s): Travis J. Riedel, Lynnette C. Johnson, John Knight, Roy R. Hantgan, Ross P. Holmes, W. Todd Lowther
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0242383

The crystal structure of mouse IRG1 suggests that cis-aconitate decarboxylase has an open and closed conformation
Cited by: 4
Author(s): Hye Lin Chun, So Yeon Lee, Ki-Hwa Kim, Chang Sup Lee, Tae‐Jin Oh, Hyun Ho Park
Software Mentions: 2
Published: almost 6 years ago

10.1089/ars.2017.7104

Inhibition of Diverse DsbA Enzymes in Multi-DsbA Encoding Pathogens
Cited by: 33
Author(s): Makrina Totsika, Dimitrios Vagenas, Jason J. Paxman, Geqing Wang, Rabeb Dhouib, Pooja Sharma, Jennifer L. Martin, M.J. Scanlon, Begoña Heras
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0098634

Insights into Alpha-Hemolysin (Hla) Evolution and Expression among Staphylococcus aureus Clones with Hospital and Community Origin
Cited by: 31
Author(s): Ana Tavares, Julius Nielsen, Kasper Boye, Susanne Mie Rohde, Ana Cristina Paulo, Henrik Westh, Kristian Schønning, Hermı́nia de Lencastre, Maria Miragaia
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0181551

Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain
Cited by: 8
Author(s): Amélie Wallenhammar, Madhanagopal Anandapadamanaban, Alexander Lemak, Claudio Mirabello, Patrik Lundström, Björn Wallner, Maria Sunnerhagen
Software Mentions: 2
Published: about 9 years ago

10.1128/AAC.00123-20

Structure and Molecular Recognition Mechanism of IMP-13 Metallo-β-Lactamase
Cited by: 8
Author(s): Charlotte A Softley, Krzysztof Żak, Mark J. Bostock, Roberto Fino, Richard Xu Zhou, Marta Kolonko, Ramona Mejdi-Nitiu, Hannelore Meyer, Michael Sattler, Grzegorz M. Popowicz
Software Mentions: 2
Published: over 6 years ago

10.1107/S2059798320016368

Macromolecular crystallography using microcrystal electron diffraction
Cited by: 9
Author(s): Max T. B. Clabbers, Hongyi Xu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0251459

Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc
Cited by: 5
Author(s): Erik I. Hallin, Sigurbjörn Markússon, Lev Böttger, Andrew E. Torda, Clive R. Bramham, Petri Kursula
Software Mentions: 2
Published: over 5 years ago

10.1107/S0907444913001479

Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data
Cited by: 79
Author(s): Qun Li, Qinglian Liu, Wayne A. Hendrickson
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0081904

New Conformational State of NHERF1-CXCR2 Signaling Complex Captured by Crystal Lattice Trapping
Cited by: 10
Author(s): Yuanyuan Jiang, Guorong Lu, Laura Trescott, Yuning Hou, Xiaoqing Guan, Shuo Wang, Angelique Stamenkovich, J.S. Brunzelle, Nualpun Sirinupong, Chunying Li, Zhe Yang
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0004656

Unusual Armadillo Fold in the Human General Vesicular Transport Factor p115
Cited by: 25
Author(s): Harald Striegl, Yvette Roske, Daniel Kümmel, Udo Heinemann
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0076876

Inhibition of Influenza A Virus Infection In Vitro by Peptides Designed In Silico
Cited by: 23
Author(s): Rogelio López-Martínez, G. Lizbeth Ramírez-Salinas, José Correa‐Basurto, Blanca Lilia Barrón
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0114373

Crystal Structure of the Fibre Head Domain of the Atadenovirus Snake Adenovirus 1
Cited by: 15
Author(s): Abhimanyu Singh, Rosa Menéndez-Conejero, Carmen San Martín, Mark J. van Raaij
Software Mentions: 2
Published: almost 12 years ago

10.1107/S2059798315021683

<i>In meso in situ</i>serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures
Cited by: 89
Author(s): Chia‐Ying Huang, V. Oliéric, Pikyee Ma, Nicole Howe, Lutz Vogeley, Xiangyu Liu, Rangana Warshamanage, T. Weinert, Ezequiel Panepucci, Brian K. Kobilka, Kay Diederichs, Meitian Wang, Martin Caffrey
Software Mentions: 2
Published: almost 11 years ago